Sunday, December 27, 2009

I recently received some unsolicited e-mail from Philip Skell, an elderly chemist who use to teach at Penn State, and a minor ID creationist. I have to admit, it was a bizarre experience.

Skell is well-known for his monomania: claiming that the theory of evolution is not relevant to medicine or experimental biology, and repeating this claim over and over again in numerous articles and op-eds. This, despite the fact that Skell is not a physician or biologist, and, as far as I am aware, has no training in these subjects. But he does like to flaunt his membership in the National Academy of Sciences.

He started off by saying "You may find the attached essay pertinent to your recent writings concerning the David Koch project." -- which was strange, because I have never written about David Koch or his "project". He then signed off as "member, NAS" and attached one of his anti-evolution opinion pieces, this one published in the journal Politics and the Life Sciences. There is nothing really new in it; Skell made the same points in an earlier piece in The Scientist, and he's recently made them again in an issue of that eminent scientific journal, Forbes.

However, Skell's claims are strongly disputed by actual biologists. For example, Nesse and Williams, in their book Why We Get Sick: The New Science of Darwinian Medicine, explain in detail how understanding evolution contributes to the improved practice of medicine. P. Z. Myers, in twodifferent posts, has explained in detail why Skell is wrong. And Gary Hurd has also pointed out Skell's misrepresentations.

When I mentioned this to the good Prof. Skell, what happened? Like the brave Sir Robin, he ran away in a huff: "As a follower of PZ you have no intellectual honesty. I prefer not to hear further from the likes of you. Sayonara!!!"

Poor Dr. Skell. He's used to intimidating the rubes with his degree and his NAS membership. But when somebody who actually knows something about the subject is cited, he vanishes in a puff of smoke and three exclamation marks.

Philip Skell - the cowardly creationist.

[For more Skell sessions, see his encounter with Jerry Coyne and his ideas being disowned by a member of his own family.]

Saturday, December 26, 2009

Meyer claims information can only come from a mind. But this is clearly not true. For example, meteorologists collect information all the time about the environment: wind speed, wind direction, precipitation, etc. Based on this information, they make predictions about the weather. But this information did not come from a mind - it came from the environment.

O'Leary is unable to refute this argument, so all she can do is babble in response, as follows:

What mind indeed? If we experience either snow or dull, freezing rain here tomorrow, why should I be surprised? This is the season officially known as winter.

Well, that certainly showed me!

When confronted with my simple counterexample to Meyer's silly claim, it seems intelligent design advocates have three choices:

1. They can deny that things like wind speed, wind direction, etc. are actually information. Then they have to claim that weather forecasters make their predictions without any information as input at all. This hardly seems like it will convince anyone.

2. They can claim that the physical world's attributes are the products of a mind. But then everything is designed, so it is pointless to claim they have a novel argument for the designedness of biological organisms, since their claim is universal.

3. They can concede that wind speed, wind direction, etc. are information, but not the particular kind of information they had in mind. This is not likely to convince anyone either, since by Meyer's own definition these measures qualify as information. Nor is it likely to convince anyone who has examined the many critiques of Dembski's CSI.

So expect the intelligent design advocates to resort to more childish tactics. Already the commenters have taken to making fun of my name, and calling me stupid and dishonest. Yup, that's the way to answer the argument.

Friday, December 18, 2009

Imagine that you're the "Secretary of State for Family" in France, and you're caught fibbing on video. An indignant citizen then comments "Hou la menteuse" (Oh, the liar!) on the website. What do you do?

Why, you subpoena the Internet provider to get the commenter's IP address, obtain her identity, and sue her for "public insult towards a member of the ministry", of course!

That's what creepy politician Nadine Morano did to Dominique Broueilh in France. Her appalling suit inspired Sarkozy adviser Henri Guaino to suggest that scrutiny by ordinary citizens on the Internet represented "the beginnings of totalitarianism". Come to think of it, maybe he deserves the award.

Morano has since dropped the suit, and the comments on the website continue to pile up - the latest victim of the Streisand effect.

Friday, December 11, 2009

For the last few years I've been editing a mathematical journal - the Journal of Integer Sequences, which is a true open-access journal. Neither authors nor readers are charged; it is completely free.

Much of my time is spent dealing with referees: choosing them, trying to get them to agree to referee a paper, reading their reports, and sending them to authors. Along the way, I've had a number of interesting experiences: like the time I kept pursuing a referee despite the fact that he was dead, and the referee who sent me a report on a completely different paper that I had not sent.

I think I now have enough data to list five laws of choosing referees:

1. In general, famous mathematicians make lousy referees. (Of course, there are exceptions.) Famous mathematicians have a lot of demands on their time, which means they probably won't even answer your request to referee a paper. If they do respond, they'll probably say no, because they're so busy doing important work. If they do accept, they'll probably take a long time. Because they're famous, they're probably really bright - much smarter than me and probably the author of the paper - so if they do write a report, it tends to be really short, snarky, and dismissive of the results.

2. Graduate students make good referees in one respect: they tend to read the paper really carefully, and are good at spotting sections where the argument is incorrect or unclear. But they rarely have the mastery of the literature needed to know if something is new or original.

3. If you have to ask a potential referee several times whether they're willing to referee a paper, then don't bother phoning them or making much more effort to contact them. If they're so disorganized and impolite that they refuse to tell you yes or no quickly, then they'll never produce a report.

4. Referees from Asia tend - generally speaking - to write extremely short reports that are rarely helpful. Whether this is a function of the culture, or whether they're embarrassed by their English skills, or something else, I don't know. In contrast, eastern Europeans generally write good and helpful reports, despite their lousy English skills.

5. The worst referees of all are the ones that agree to referee the paper and then keep stringing you along for month after month, each time claiming that they're almost done the report, and it will be coming shortly. I once wasted 9 months pursuing a referee who kept claiming it would be there next week. So if you can't get a report from the referee within a month of the time they originally promised, give up - and tell the referee why you're giving up on them.

I attended The Great Climate-Gate Debate yesterday at MIT. It was videotaped, so maybe eventually it will be available online, but for the moment, here is a brief and possibly inaccurate description based on notes I took during the event.

It wasn't really a debate. None of the participants really addressed each other in any substantial way. It consisted of 5 10-minute presentations, followed by questions from the audience. My summaries of each speaker are given below, with my comments in italics.

The first speaker was Kerry Emanuel, a professor of atmospheric sciences at MIT. He contrasted the situation in science with politics. In science the truth will win out; but politics enters the scence because the coal industry will lose billions. They spend lavishly in campaigns to protect themselves. Just like the tobacco industry, which set up fake grassroots organizations to deny the connection between smoking and lung cancer, the anti-AGW [anthropogenic global warming] crowd sets up similar organizations. The tobacco industry's efforts were successful: it took decades before smoking began going down.

The anti-AGW efforts are even more successful. The scientific consensus is clear. All scientific organizations agree. Yet polls show that the percentage of the American public who believes that global warming is human-caused is decreasing. How did this come to pass? By deployment by vested interests of advertising techniques. Terminology is controlled. Deniers are called skpetics. Most of the people called skeptics are not really skeptics, since no evidence would persuade them. By contrast, people who take the problem seriously are called "alarmists". The public relations machine has been successful in branding atmospheric scientists as out-of-touch liberals who want to return to an agrarian society. On the other hand, deniers are compared to Galileo.

The thousands of e-mail messages that were stolen show scientists at work. Among them are a few lines of scientists showing human failings. Scientifically it means nothing. But it is a windfall for the anti-AGW machine.

The next speaker was Richard Lindzen, professor of meteorology in the Department of Earth Sciences at MIT. He started by denying that there is an anti-AGW machine. [Hard to take this seriously: exactly who does Lindzen think is behind ads like the ones reported here?] He doesn't know what AGW has to do with smoking. [It's because, as Emanuel clearly stated, the techniques used by the deniers on both sides are similar. Also, Lindzen himself -- a smoker -- is famous for his skepticism on the link between smoking and cancer, so I imagine it was a little dig at him.] It's a red herring. What we're here to talk about is e-mail and computer code. There's no chance that some machine unknown to Lindzen is behind this.

The relaeased documents are unambiguously dealing with things that are unethical and illegal. There is no good in any scientific organization endorsing this. The documents show scientists manipulating raw temperature data. [Uh, manipulation of raw data goes on all the time; that's why it's called raw data.] They refused to allow outsiders access to data. [Uh, because they signed a non-disclosure agreement]. They destroy data rather than release it. They don't allow responses to their papers to be published. This is not ethical.

What are the implication? It won't have much influence on Copenhagen. You don't get 20,000 people to change direction. Very few people can read these documents and not conclude that there was something bad going on. There is diminishing popular support for this issue. This is not mass hysteria, this is elite hysteria. The notion that science is prone to cheating and if Kerry [Emanuel] is right, that this is endorsed by scientific organizations, is detrimental to science. If your information environment is NPR and the New York Times, you believe one thing. If your information environment is talk radio, you believe another. He recommended Anthony Watts' blog. It's good that ordinary people can check the temperature measurements; people are discovering bizarre changes to the data.

Next was Judith Layzer, who is a professor of Environmental Policy at MIT. [I didn't get much out of what she was saying.] She is an observer of science. She concluded by saying that scientists are fallible but offer the best hope of understanding the natural world.

Next was Stephen Ansolabehere, professor of Political Science at MIT. [I didn't get much out of what he said, either.] Scientific evidence hasn't been vetted the way it should. So far it's in scientific journals, congressional committees, etc., not vetted in public the way it should be. However, the e-mails don't affect most of the data people are using. But it does raise a fundamental question of science - the importance of scientific standards. It raises the question of how science can maintain its standards as it gets pulled into public debates. Who is going to police scinece and maintain its public credibility? One of the great crimes is the violation of the standard of replicability. Who is going to discipline the scientists? What will the response be from scientific academies?

The last speaker was Professor of Atmospheric Science at MIT. He began speaking about the hockey stick. In answer to Lindzen, we care about a few tenths of a degree because it is important to compare current temperatures with historical data. He looked at the emails and was disturbed. He discussed the disagreement between Michael Mann & McIntyre-McKittrick. Around 1850, the blade "sticks out" (referring to rise in northern hemisphere temperatures). It did disturb him when looking at the emails to see the personal nature of the discussion. Are some of the e-mails unprofessional? Yes.

Were the people successful in preventing publication? Five papers by McIntyre were published and discussed in the 4th IPCC. There's a signficant case to be made that temperatures are higher - the "blade" has survived the scrutiny. It's unclear if the "handle" is straight or broken. People will think of other proxies. Were the people successful in the endeavor that seemed to be stated in the emails? No.

Was the research at E. Anglia critical to the case for climate change? He looked at this because he gave testimony about climate change. There are many different lines of evidence. Several independent data sets exist - the work at UEA is not the only group. Without even including analysis from UEA the conclusion that most of the warming is human-caused remains robust. Since 1997 to 2007 when he gave testimony in the House Ways and Means Committee, he changed his mind. The new data was enough to convince me that there was statistical significance to the conclusion. His view is that we have no other planet to retreat to if we are wrong. If we screw up this planet, what do we do?

Has the integrity at the IPCC been compromised by these revelations? UEA people were involved at IPCC. IPCC is arguably the most influential. Those emails did not lead to McIntyre-McKittrick papers not being discussed. Answer is no.

Is public perception of climate science affected? Media ability to scrutinize is a problem. E-mails contain a lot of juicy soundbites who want to write stories. Answer is yes.

Can we do better? Climate researchers need to step back from the tendency to polarization. Scientists have got to stop that process. That means having mutual respect. I have great respect for both of these guys (Lindzen and Emanuel) as excellent scientists. Find additional ways to communicate conclusions and the ways conclusions were reached. A single paper is not enough. Many results needed before consensus is reached.

Peer-reviewed literature is where science is done. Not in blogs or opinion pieces. These should not be the source of information. Can we do better? The answer is yes.

After the presentations, there were many questions. I did not take notes during the Q & A. If the event video is ever shown, you can see me asking a question towards the end.

Finally, one minor note that bugged me. Speakers referred to each other using their first names, making it hard to follow. If only the organizers had bothered to put a card in front of each speaker, with their full name, the audience would have been much better off.

Wednesday, December 09, 2009

Hey - this is great. Chrystal's Algebra, an old textbook that has wonderful chapters on continued fractions and one that influenced Ramanujan, is available freely online here at the University of Pennsylvania.

If you want to go directly, try here for Volume 1, and here for Volume 2. The chapters on continued fractions are 32-34 in Volume 2.

Tuesday, December 08, 2009

Every year, the Computing Research Association gives out awards for the best research done by undergraduates in North America. This year, my student Elyot Grant shared the top prize for males with Matt McCutchen from the University of Maryland.

Here are some of the problems Elyot worked on. First, he found a quadratic lower bound corresponding to a famous 1977 theorem of Entringer, Jackson, and Schatz that states that every binary string of length ≥ n2 + 6n contains an abelian square of order ≥ n. (An abelian square is two consecutive blocks where one is a permutation of the other; for example, reappear is an abelian square, as reap is a permutation of pear.)

Second, a problem of Alon and Spencer shows that for all ε > 0, there exists an infinite binary word such that any two consecutive blocks xx' of the same length t > N differ in at least (1/2 - ε)t positions. This raises the natural question, can the bound of (1/2 - ε) be replaced by a number > 1/2? Elyot proved the answer is no, using an extremely clever idea. This paper, co-written with my postdoc Thomas Stoll, appeared in the journal Acta Arithmetica.

Third, Elyot found beautiful results on “open” and “closed” languages, which are analogous to open and closed sets in topological spaces. His work with me and John Brzozowski was accepted for the DLT 2009 conference, and Elyot gave a beautiful talk on the subject.

Sunday, December 06, 2009

Every town's got one -- the prudish busybody who can't stand the fact that information about sex is available at the public library.

So when Marti Shigley found a copy of Eric Marlowe Garrison's Mastering Multiple Position Sex in her public library, she did what every censor wants to do: she checked the book out and is refusing to return it. She reportedly said, "When I opened it, I could not believe how graphic it was, and I thought my word if one of those kids had picked this up and looked inside of it they would have been ruined for life."

Shigley is a criminal and a first-class jerk. But what's even worse is that the local TV station, reporting on Shigley's crime, blotted out portions of the book's cover and refused to provide its title.

Saturday, December 05, 2009

Just back from the Newton Public Library book sale, held in Auburndale. I love book sales, because they're an opportunity to build my pseudoscience collection without directly subsidizing the authors.

I picked up the 992-page The Evolution Handbook by Vance Ferrell, which is published an outfit called "Evolution Facts, Inc." and headquartered in Altamont, Tennessee. They seem to have a website, too.

What's fun about creationist books is that it's so easy to refute them. To show this, I conducted an experiment: I turned to three pages at random, and looked for the first lie I could find. Here are the results:

p. 176: "...the experts have so far been unable to agree on the length of a rubidium half-life. This renders it useless for dating purposes. This is because the samples vary so widely. Abrams compiled a list of rubidium half-lives suggested by various research specialists. Estimates, by experts of the half-life of rubidium varied between 48 and 120 billion years! That is a variation spread of 72 billion years: a number so inconceivably large as to render Rb-Sr dating worthless."

Reponse: BOGUS. In the early days of nuclear chemistry it was hard to be precise about very long half-lives, but better chemical and radiometric techniques have long removed the uncertainty. I looked online for Rb-87 half-lives, and I found strong concordance: for example, 4.7E10 and 4.88E10. This page discusses a variety of different estimates of the decay constant, all of which are within about 10% of each other. I don't know who "Abrams" is or where the estimate of 120 billion years came from, and The Evolution Handbook contains no reference on this point.

p. 531: "About 15 years before his [Dubois'] death, and after most evolutionists had become convinced that his find was nothing more than bones from a modern numan, Dubois announced his conviction that the bones belonged to a gibbon!"

Response: BOGUS. Paleontologists believe the remains are about 700,000 years old, although there is still some controversy about the femur. The claim about the gibbon is false.

p. 801: "Darwinism unleashed a moral holocaust upon the world, one which deepens with each passing decade."

Response: BOGUS. People have been killing each other since the dawn of mankind. Evolution is a scientific theory and a description of the world, not a guide about how to behave. The atrocities blamed on "Darwinism" are actually due to nationalism, religion, or political opportunism.

Not bad, eh? Three pages, three lies. Creationists have to lie, because the evidence is all against them.

Friday, December 04, 2009

These creeps have a rule against long hair for boys in their schools. But it's not the school's business to govern how students can wear their hair. If there are concerns, such as head lice, these can easily be handled by techniques used in other schools.

In this case, the jerks at Needville enforced their rule against a kindergartner who wore his hair long in keeping with his parents' religion. Luckily, the ACLU was there to defend the kid's rights. [Are you a member of the ACLU yet? If not, send them a donation.]

A judge ruled in favor of the kid, but the school appealed. Now the case is being heard in the Appeals Court.

I sure hope Needville gets their butts kicked back to Texas. Why school administrators delight in enforcing these bizarre and arbitrary rules against their students is beyond me. Schools should be about learning and helping students achieve their potential, not authoritarian discipline.

Thursday, December 03, 2009

The always-repulsive David Gelernter, who was attacked by the Unabomber and never seems to have gotten over it, appeared today on the NPR show "On Point".

Here's Gelernter on tolerance (from the 42:30 mark of the show):

David Gelernter: ... One of the most important verses in the Bible which says apply your own experience, you must be kind to strangers because you were strangers yourselves, you know what it's like. Tolerance is a Jewish idea, and emerged in this country from the Biblical community.

Caller Kathy: ... I'd like to comment on an earlier caller who was remarking about the disconnect between the principles that are in the Bible, and the actualities, especially the situation in Israel with the Palestinians. And your guest said that obviously that person had not been there and didn't know that Israel had the most just army in the world.

Well, number one, I'm Jewish, number two, I have been there. And I will tell you that all of the commentary about how people should behave has been thrown out the window by the government and the military of Israel. And I have seen it with my own eyes - I'm not stupid. All you have to do is go through the separation wall which is an apartheid wall and see the miserable condition of Palestinians who are Muslims and Christians and see what is being done to them by the occupying Army of Israel.

Tom: Kathy, we've got the gist and our time is very short. Thank you for calling. David, how do you respond?

David Gelernter: It's always been the curse of Jews that the most vicious haters of the Jewish community have often been Jews themselves.

There's no question in my mind that Israel gets treated shabbily by the American Left, and Israel's record is much better than that of its neighbors. But on the other hand, one can't deny that there have been human rights violations against the Palestinians, of which house demolitions are a prominent example. David Gelernter's response here is grotesque and facile, and doesn't deal honestly with the question.

Monday, November 30, 2009

Scientists point out, quite rightly, that the religio-political charade known as "intelligent design" (ID) is not good science. But how do we know this?

One of the hallmarks of science is that it is fruitful. A good scientific paper will usually lead to much work along the same lines, work that confirms and extends the results, and work that produces more new ideas inspired by the paper. Although citation counts are not completely reliable metrics for evaluating scientific papers, they do give some general information about what papers are considered important.

ID advocates like to point to lists of "peer-reviewed publications" advocating their position. Upon closer examination, their lists are misleading, packed with publications that are either not in scientific journals, or that appeared in venues of questionable quality, or papers whose relationship to ID is tangential at best. Today, however, I'd like to look at a different issue: the fruitfulness of intelligent design. Let's take a particular ID publication, one that was trumpeted by ID advocates as a "breakthrough", and see how much further scientific work it inspired.

Putting these considerations aside, what I want to do here is look at every scientific publication that has cited Meyer's paper to determine whether his work can fairly said to be "fruitful". I used the ISI Web of Science Database to do a "cited reference" search on his article. This database, which used to be called Science Citation Index, is generally acknowledged to be one of the most comprehensive available. The search I did included Science Citation Index Expanded, Social Sciences Citation Index, and Arts & Humanities Citation Index. Even such a search will miss some papers, of course, but it will still give a general idea of how much the scientific community has been inspired by Meyer's work.

I found exactly 9 citations to Meyer's paper in this database. Of these, counting generously, exactly 1 is a scientific research paper that cites Meyer approvingly.

By contrast, let's compare Meyer's work with another paper, in the same field, of roughly the same length, and published in the same year:

This paper has been cited 60 times since 2004, according to ISI Web of Science, by researchers writing in journals such as Systematic Biology, Journal of Anatomy, Bulletin de la Société Géologique de France, Proceedings of the Royal Society B - Biological Sciences, Journal of Morphology, Zootaxa, Journal of Ornithology, Naturwissenschaften, Journal of Vertebrate Paleontology, etc., etc. Clearly there is a substantial difference in opinion of this paper, versus Meyer's.

Now let's look at all 9 papers that have cited Meyer's work, as reported by ISI Web of Science. I have read every paper, except paper 4 (Luskin); for that paper I had to be content with an abstract.

2. K. M. Helgen, "Meyer paper: don't hang the Soc. Wash. out to dry", Nature432 (7020) (Dec 23 2004), 949. A letter to the editor defending the reputation of the journal that published Meyer's article. Money quote: "Given the Proceedings’ taxonomic focus, Meyer’s ID paper is clearly out of place. Its publication represents a lapse of the journal’s usual editorial policies, and has been swiftly repudiated (www.biolsocwash.org). However, although the publication of Meyer’s paper is lamentable, it need not be used to trivialize the Proceedings’ long, respectable and ongoing tradition of cataloguing global biodiversity." Not a scientific research paper.

3. Mark Terry, "One nation, under the designer", Phi Delta Kappan86 (4) (Dec 2004), 264. Abstract. Full paper (subscription required). This journal is a professional journal for educators. The paper's subtitle reads, "Mr. Terry alerts readers to a new, more insidious anti-evolutionist strategy. And the redefinition of science is only the first step." Meyer's paper is discussed, as follows: "The supposed "scientific revolution" is a creation of public relations. A science teacher cannot go to any major science journal or scientific organization and find out about all this new research - because there is none. In the fall of 2004 an ID article by a Discovery Institute Fellow appeared in the Proceedings of the Biological Association of Washington, a venerable but formerly obscure journal dealing with subtle taxonomic issues. The flurry of responses to the article gives a good picture of the current state of ID as science: the governing council of the journal almost immediately disavowed the article's publication." Not a scientific research paper.

4. C. Luskin, "Alternative viewpoints about biological origins as taught in public schools, Journal of Church and State47 (3) (Summer 2005), 583-617. First page. A journal of law and social science. Luskin is "Program Officer in Public Policy and Legal Affairs" at the Discovery Institute. Not a scientific research paper.

5. B. H. Weber, "Emergence of life", Zygon42 (4) (Dec 2007), 837-856. Zygon is self-described as a journal of "religion and science", but I would consider it a philosophy journal. A review article. Of the nine papers, this is the one that is the closest to a scientific research article that cites Meyer approvingly: "The emergence and increase of novel, specified, functional information remains the crucial issue." He thinks that Meyer's questions have been answered by "the new science of emergent complexity".

6. J. Koperski, "Two bad ways to attack intelligent design and two good ones", Zygon43 (2) (June 2008), 433-449. Again, Zygon is self-described as a journal of "religion and science", but I would consider it a philosophy journal. This article focuses on the rhetoric of intelligent design and its opponents. Not a scientific research paper.

7. Emilia Currás and Enrique Wulff Barreiro, "Integration in Europe of human genetics results obtained by Spaniards in the USA: A historical perspective", Scientometrics75 (3) (2008), 473-493. This is the strangest paper of the nine. It purports to be about "the mobility of Spanish biochemists from Europe to the United States over the past 80 years". It cites Meyer as follows: "In the context of cancer research, the (chemical and reductionist) search for the molecular basis of cancer induction is combined with the holistic vision of the close relationship between form and function in physiology [Shimkin, 1974; Meyer, 2004; Marra & Boland, 1995]". Although it is about "form", Meyer's paper doesn't mention "cancer" or "physiology" at all. Perhaps the citation was really meant to refer to something completely different? In any event, this paper is more a historical discussion, not a scientific research paper.

8. S. L. Shafer, "Critical thinking in anesthesia: Eighth honorary FAER research lecture", Anesthesiology110 (4) (2009), 729-737. Full paper here. An article criticizing various anti-scientific trends. Here is how he cites Meyer: "One can find many Web sites devoted to intelligent design. However, the story in the peer-reviewed literature is quite different. Of 99 articles identified by a PubMed search of intelligent design (on November 14, 2008), the majority are defenses of evolution against claims of intelligent design. Not appearing in the search is the single scientific article supporting the claims of intelligent design written by Stephen Meyer of the Discovery Institute. This article was published without peer review in a nonindexed journal and was subsequently retracted by the journal for insufficient scientific merit." Not a scientific research paper. [Update: Shafer's claim about "published without peer review" is not correct, and the paper was not actually formally "retracted". "Disavowed" is more like it.]

9. Juan E. Carreño, Fernando Hansen, et al., Some considerations about the theory of intelligent design, Biological Research42 (2) (2009), 223-232. Full paper here. An article, critical of intelligent design, in an obscure Chilean biology journal. However, the topic is more about philosophy than science. Money quote: "We also reject the claim that ID is a legitimate scientific theory, because it does not exhibit the classical characteristics that a scientific kind of knowledge must have." Not a scientific research paper that cites Meyer approvingly.

The grand total: exactly 1 paper (Weber's) can be said to be a scientific paper that cites Meyer approvingly, and even that is subject to debate.* This meager record does not support the claim that ID is a scientific revolution with far-reaching consequences.

ID advocates are constantly telling us that intelligent design is a new scientific paradigm that will prove fruitful. Five years after ID's flagship "peer-reviewed" paper, that does not seem to be the truth.

* No doubt ID advocates will produce other papers, published in obscure venues, that cite Meyer, that I missed. For example, Google scholar lists a few more, including:

10. Fernando Castro-Chávez, "Hepatology Microarrays, antiobesity and the liver", Annals of Hepatology 3 (4) (Oct-Dec 2004), 137-145. Full paper here. A case of inappropriate citation. The only citation to Meyer comes in the final paragraph, which reads "... to better describe the identity and function of genes and genomes, composers of a natural, complex, and precise biological software that as a genetic program, contributes to the healthy programming and the pathological reprogramming of life." The author appears to be an intelligent design advocate. I predict that inappropriate citation -- the bogus insertion of citations to pro-ID papers in irrelevant contexts -- will become more popular in the future, as creationists attempt to bolster their case that ID is scientific.

But ISI Web of Science also misses a number of articles critical of Meyer. In any event, the citations I have found do not support the extravagant claims made for ID and for Meyer's article. So far, ID is not proving frutiful for science.

I gave an example that trivially refutes Stephen Meyer's claim that "information always comes from a mind": weather prediction. Meteorologists record information such as wind speed, wind direction, and temperature to make their predictions. Under both the informal definition of information used in everyday life, and the formal technical definitions of "information" universally accepted by mathematicians and computer scientists, these quantities indeed represent "information". What is the response?

Of course, it's the old information bait-and-switch trick: Dembski is now claiming that my example was "unspecified information", whereas Meyer was talking about "specified information".

Dembski is an old hand at the information bait-and-switch game, as Elsberry and I showed in detail in our peer-reviewed article. He moves from one definition to another seamlessly, as it suits him, for whatever argument is at hand. This is most apparent in his estimation of probabilities, where he switches back and forth between the uniform probability interpretation and the causal-history interpretation, depending on which one gives the answer he requires. We discuss this at length in our article.

Furthermore, the notion of "specification" comes from Dembski himself, and as Elsberry and I showed, it is completely incoherent. Nobody can say whether a given string is "specified" or not, and "specification" fails to have the properties Dembski claims it has. No mathematician or computer scientist, other than Dembski and his intelligent design friends, uses Dembski's measure or does any calculations with it. To pretend that it is meaningful is not honest.

Just to give one example, here is Dembski and his deep technical and mathematical "proof" that "the [sic] bacterial flagellum" is specified:

"At any rate, no biologist I know questions whether the functional systems that arise in biology are speciﬁed." (No Free Lunch)

So, a challenge: which, if any of the following strings constitute "specified information"? Be sure, in your answer, to give all the things that Dembski says are required before one can be sure: the space of events, the rejection function, the rejection region, the "independently-given" specification, the relevant background knowledge, the independence calculation, and so forth.

Meanwhile, Dembski needs to inform his acolyte "Joe G", who thinks that the proper definition of "information" is "the attribute inherent in and communicated by one of two or more alternative sequences or arrangements of something (as nucleotides in DNA or binary digits in a computer program) that produce specific effects". Well, by that definition, my example of the information used in weather prediction is indeed information -- there are many alternatives in wind speed, direction, and temperature, and no one can doubt that different arrangements of these quantities produce different effects -- namely, different weather.

Joe G, get with the program! Just say my example is "unspecified", and be done with it! No need to trouble yourself with actual thinking.

Thursday, November 26, 2009

Steven Goldberg is an American sociologist. In his book, When Wish Replaces Thought, he proposes the following argument against descriptivism, which he seems to think is completely decisive. I found the argument interesting, because it attempts to use self-reference in much the way Turing's proof that the halting problem is unsolvable does. Unfortunately, Goldberg's argument is flawed in several respects.

Here is the relevant passage, which appears on pp. 193-194:

"People with more than a passing interest in words fall into two groups, prescriptivist and descriptivist. The prescriptivist believes that there is an ideal of correctness in the use of words - shifting and temporally based as it ultimately may be. The descriptivist finds the concept of "correctness" elitist at best and, more often, incomprehensible.

"The one inviolable rule of descriptivism is this: There are no correct definitions, meanings, or usages other than those used by people-in-general; any attempt to substitute a definition, meaning, or usage for that used by people-in-general is invalid. Where the prescriptive subordinates popular usage to correct usage, the descriptivist denies to correctness and all other criteria parity with use by people-in-general.

"Now consider what happens when you ask a descriptivist how he defines "dictionary" in his descriptivist dictionary.

"The descriptivist might, as his inviolable rule says he must, accept the definition of "dictionary" used by people-in-general. If he does this, he will define "dictionary" as people-in-general really do, as giving correct definitions, correctness being determined by a literary elite. The descriptivist must accept the view of people-in-general that there is a correct usage -- in this case correct definitions -- because his inviolable rule requires that he accept the view of people-in-general. In granting that there is a correct usage, the descriptivist grants what his inviolable rule, his basic premise, denies.

"The descriptivist might, on the other hand, reject the definition used by people-in-general and substitute the definition of "dictionary" implied by his violable rule, the definition that denies there there is a "correct" usage other than that used by people-in-general. But if he does this, he does the one thing that his inviolable rule prohibits. He substitutes a "correct" definition whose existence his basic premise denies for the only definition that his basic premise -- his inviolable rule -- grants as legitimate, the definition used by people-in-general.

"The descriptivist cannot argue that people-in-general are incorrect in defining a "dictionary" as giving correct usage because "incorrect" (or "wrong") has no meaning in the descriptivist universe (except, perhaps, to describe misrepresentation of the usage of people-in-general, which is just what the descriptivist does if he alters the definition of "dictionary" used by people-in-general; people-in-general cannot, according to the descriptivist premise, be incorrect).

"Whether the descriptivist accepts the definition of "dictionary" used by people-in-general or rejects the definition used by people-in-general, the descriptivist's descriptivism is exposed as rotten at its core. Note that the contradiction is not merely an oddity relevant only to a single definition. The problem of defining "dictionary" is but a focused view of a contradiction that infuses all of descriptivism and that can be stated without reference to a definition of "dictionary". The general contradiction is that descriptivism is founded on an axiom that accepts "A" (popular usage) and rejects "B" (any other authority or criterion for correctness) even when acceptance of "A" commits descriptivism to an accepance of "B", which is rejected by the axiom ("A") that requires its acceptance."

I think this argument is flawed for a number of reasons. Here are a few.

1. I think Goldberg caricatures what descriptivists believe. A descriptivist wouldn't say that meaning is determined the use of "people-in-general", because words don't have single meanings. For example, what if exactly 50% of "people-in-general" think a word means one thing, while exactly 50% of "people-in-general" think it means another? Then there is no one meaning held by "people-in-general" at all. For another, words have multiple meanings and shades of meaning. Sometimes these meanings can even be the opposites of each other. What, for example, do "people-in-general" mean by the word "cleave"? On the one hand, it can mean "to stick together". But it can also mean "to cut apart". Then there are words whose meanings have gradually shifted over time, such as "nubile". Originally, it meant "marriageable", but these days it seems to be used more as if it means "young and sexy".

2. I think Goldberg caricatures what "people-in-general" believe about the meaning of the word "dictionary". It may well be that "people-in-general" think of a dictionary roughly like what Goldberg claims: as a book "giving correct definitions, correctness being determined by a literary elite". But if you ask "people-in-general" whether they think a dictionary can ever contain an incorrect definition, or is it necessarily always right, I'd be very surprised if they choose the latter option. Furthermore, there is not a single dictionary accepted by all English-speaking people, but many different ones. "People-in-general" will have to concede that these many different dictionaries may disagree on the meaning of a word. So a descriptivist may well define "dictionary" as "a book containing usually-correct definitions, approved by a literary elite" and still satisfy the beliefs of "people-in-general". But then Goldberg's "contradiction" disappears.

3. The dictionary definition of "dictionary" doesn't usually claim its definitions are correct. For example, picking a dictionary at random from the web, I find the first definition of "dictionary" as "A reference book containing an alphabetical list of words, with information given for each word, usually including meaning, pronunciation, and etymology." Given that, maybe "people-in-general" don't assume what Goldberg claims they do.

4. "People-in-general" may well believe that a word has a certain definition but that does not necessarily mean that the object that the word refers to actually exists. For example, "people-in-general" might define "unicorn" as "a goat-like animal with magical powers and a single horn", but that doesn't mean that unicorns actually exist or have magical powers. Acknowledging this doesn't violate the descriptivist position; the descriptivist need not be a moron. So "people-in-general" may believe that a dictionary is a book "giving correct definitions, correctness being determined by a literary elite", but that doesn't necesssarily believe that such a book actually exists. Thus, a descriptivist can, without fear of contradiction, believe both that "people-in-general" think "dictionary" has this meaning on the one hand, and also believe that no such book as described by "people-in-general" actually exists in the real world.

So while I find Goldberg's attempt interesting, I think it is a failure.

Does Nagel have any biological training? None that I could see. Does he know anything about evolution or abiogenesis? Not if he thinks Meyer has any valid contribution to make. Did he bother to check if biologists think Meyer's book is a good contribution to the literature? I doubt it. Did Nagel spot all the phony claims Meyer makes about information? I doubt it again.

Just to cite one: Meyer claims, over and over again, that information can only come from a mind -- and that claim is an absolutely essential part of his argument. Nagel, the brilliant philosopher, should see why that is false. Consider making a weather forecast. Meteorologists gather information about the environment to do so: wind speed, direction, temperature, cloud cover, etc. It is only on the basis of this information that they can make predictions. What mind does this information come from?

It's sad to see such an eminent philosopher (Nagel) make a fool of himself with this recommendation.

My barber told me, quite straight-faced, a new creationist claim. There is, he said, abundant evidence in the Torah that dinosaurs were actually demons. "No, they were just animals," I replied. Despite our disagreement, I got a good haircut.

Tuesday, November 24, 2009

I never flew into the Toronto Island airport before, but I did so for the first time on Sunday. After you land, a ferry takes you across 120 meters of water in 60 seconds. This is what the view looks like from the ferry. Not bad, eh?

By now you've probably heard the story of a man, thought to be in a coma for 23 years, who was recently "discovered" to be conscious the whole time.

Maybe so. But maybe not.

As James Randi points out, a video clearly shows that the man himself is not typing. Instead, a woman is shown using a technique called "facilitated communication", where she moves his hand to type on a keyboard. He is not moving his hand independently.

That's the title of a new book by Harvey Silverglate. The subtitle is "How the Feds Target the Innocent".

There's no question that overzealous and politically-motivated prosecution has destroyed the lives of many innocent people. One prominent example discussed by Silverglate is former Alabama governor Don Siegelman, whose conviction on corruption charges was almost certainly engineered by Karl Rove and the Bush White House.

Despite this, I was disappointed by the book. For one thing, the title - based on a claim that the average "busy professional" "likely commit[s] several federal crimes" each day, is simply not substantiated. The crimes discussed in this book are mostly things like overprescription of painkillers, flawed medical device manufacture, accounting fraud, etc., which are probably not the domain of the average "busy professional". For another, the focus on federal crimes leaves out some of the most egregious prosecutions, like those for copyright violation and teenagers recording their own sex acts.

But the main flaw is that I was not actually convinced by several of the cases discussed that the people charged were actually innocent or that the prosecutions were illegitimate. Some of the cases turn on strained readings of existing law, where the people involved should have known their actions were dubious. In two cases - the prosecution of Boston pols Kevin White and Thomas Finneran - Silverglate seems to suggest that influence peddling is just a normal part of city politics, and nothing to get worked up over. I don't agree. I want all politicians to keep their decisions squeaky clean and completely removed from their financial interests. They need to avoid even the appearance of conflict of interest.

So, while I agree with Silverglate's main thesis, I think some of the cases he chose were not the best examples of overzealous prosecution. Too bad - because this is an important topic that deserves a comprehensive treatment.

Saturday, November 21, 2009

Here's an interesting preprint by John Barrow about the optimal configuration of rowers to minimize "wiggle". The story was picked up by Technology Review, which you should go read first.

Ultimately, the problem comes down to assigning exactly half of the numbers from 1 through N a sign of +1, and the other half -1, so that the sum of the numbers is 0. For N = 4 there is one solution

1 2 3 4+1 -1 -1 +1

and its "reflection" that is obtained by multiplying everything by -1.

It's easy to prove that a solution exists if and only if N is a multiple of 4. For N = 8, Barrow proposes some new solutions.

There is a connection here to the Thue-Morse sequence t(i), which assigns to i either +1 or -1, according to the parity of the number of 1's in the binary expansion of i. An old theorem of D. H. Lehmer implies that

Σ0 ≤ i < 2k t(i) p(i) = 0

for any polynomial of degree < k. So in particular, the Thue-Morse sequence gives an infinite family of solutions to the wiggle-free rowing problem, whenever N is a power of 2. In particular, for N = 8, Barrow's solution (d) is given by the Thue-Morse sequence.

As an aside, Barrow implies something about the complexity of the problem in his abstract. He says, "We show that the problem of ﬁnding the zero-moment rigs is equivalent to a version of the NP-complete Subset Sum problem." No, not really. He showed that his problem is a special case of the subset-sum problem, which says nothing at all about its complexity. After all, his problem is also a special case of the halting problem! And in any event, since it is easy to show that solutions exist if and only if N is a multiple of 4, the decision problem's complexity is trivial.

This is yet another example of the rule that says "Whenever scientists or mathematicians with no formal training in computer science talk about complexity theory, with high probability they are quickly going to say something stupid." For another example, see here. Of course, if I were to write about physics, no doubt I would say something equally stupid.

A few minutes later, the same guy posted the same single-word comment again. I deleted it, but noticed in the WordPress e-mail that his comment had come from an IP address at a local school. So I called the school. They were happy to have me forward the e-mail, though I wasn’t sure what they’d be able to do with the meager information it included.

About six hours later, I heard from the school’s headmaster. The school’s IT director took a shine to the challenge. Long story short: Using the time-frame of the comments, our website location and the IP addresses in the WordPress e-mail, he tracked it back to a specific computer. The headmaster confronted the employee, who resigned on the spot.

Not surprisingly, the reaction to Greenbaum's misconduct was negative. What to do? Why, shut off the comments, of course!

Wednesday, November 18, 2009

Back on my previous sabbatical, in 2001-2, I spent a couple of months reading WIlliam Dembski's book, No Free Lunch, which he was kind enough to send me. I chose to do that for a number of reasons: first, I was interested to see if his claims about a mathematical refutation of Darwinism were true; second, a sabbatical is the time to tackle some unusual project you don't usually have time for; and third, I have an interest in pseudoscience and pseudomathematics. Reading it led to some fun discussions with Wesley Elsberry and we eventually produced a long, 54-page refutation of many of Dembski's claims.

But then, what to do with it? I had heard Dembski and Ruse were co-editing a voume, so I briefly entertained the idea of submitting it for inclusion there. But I was worried Dembski would refuse because the paper was sharply critical of his work, and after talking to Ruse I had second thoughts and decided to look for another venue. We chose a journal whose subject matter included biology and philosophy, but the paper was eventually rejected -- not because of the quality of the paper, but because the referees felt that spending 54 pages to debunk what they perceived as anti-evolution crackpottery was not a good use of their journal's space.

Finally, we were invited to submit the paper to a special issue of the journal Synthese, and we did so. The paper went through multiple rounds of refereeing, with the referees suggesting that more and more be cut. Now that it has finally appeared, it is down to a measly 34 pages. Luckily the long version is still available online.

If you can't read the Synthese version because you don't have a subscription, just write me and I'll be happy to send you a copy.

This is the longest interval I've ever had between finishing a paper (2002) and the time it appeared (2009). And it's likely to be my only paper in a philosophy journal. I predict that the intelligent design community will continue to ignore all the criticisms (which have been available to them for years) and continue to pretend that CSI is actually a coherently-defined entity, and that the "law of conservation of information" holds. I predict lots of breast-beating, and excuses for not addressing our criticisms, but no response that deals forthrightly with all the errors we found in Dembski's work.

As you probably know, creationist moron Ray Comfort has created a new version of Darwin's Origin of Species with his own introduction, and his minions are now handing them out at college campuses in the US. Above is a picture taken 15 minutes ago at MIT, showing a creationist happily distributing this bizarre book.

Here's an interesting article about an apparently new blue pigment discovered serendipitously by chemists at Oregon State. The color is reported to arise from Mn3+ "introduced into the trigonal bipyramidal sites of metal oxides". The new pigment is said to be better than alternatives such as cobalt blue, ultramarine, Prussian blue, and azurite, because it is stable and non-toxic.

I'm a little skeptical that it's commercially viable, since the examples the chemists have produced so far are based on compounds using the rare metals yttrium, indium, lutetium, and gallium.

Perhaps it is just a coincidence, but there is exactly one known mineral that crystallizes in the trigonal bipyramidal form, and it is also known for its blue color: benitoite (BaTiSi3O9).

Monday, November 16, 2009

A creationist has responded to this post about the dirty rhetorical tricks of creationists, as follows:

There is really no scientific evidence that proves evolution happened. No animal has developed extra chromosomes that we have recorded and none of the findings of supposedly ancestors have any DNA evidence. Evidence does not hold up in court.

Darwin had a theory, based on observation. Fine.

Creationists have a theory based on the Bible.

Intelligent design mongers are clueless and belive in Star Trek.

No one knows where we come from, but the fact that Darwinism was used as en excuse to justify fascists regimes is a fact. They refer to Darwin as their substitute for God all the time in their literature, comparing fascism to "Survival of the Fittest. Why? He is dead, he can't defend himself.

Let me explain where they are wrong. Nature doesn't work by "survival of the fittest". "Survival of the species" trumps that. Observe bees, bacteria, herds of animals, even predators like lions depend on socialization for survival. Where is the "survival of the fittest?". The economists, in their greedy ways twist science to justify a consumerist society in which a few have wealth and the rest suffer.

It really is remarkable for its stupidity, ignorance, and arrogance, all rolled up into one. Isn't it?

This prominent building, in Boston's downtown, is probably the city's largest monument to foolishness. Although its supporters make extravagant health claims, these are not supported by evidence. Nevertheless, the group's political power has helped pass laws in dozens of states to allow it to avoid prosecution.

Sunday, November 15, 2009

You know a call for "more civility" is completely phony when the person who issues it only cites examples from one side of the debate.

That's the case with this recent opinion piece by Casey Luskin, spokesman for the Discovery Institute.

Luskin lists three examples of incivility, and all of them are from the pro-science, anti-creationist side. He fails to cite a single example of incivility from a creationist, even though there are many examples to choose from. As Wesley Elsberry has documented, Luskin's friends routinely compare evolutionary biologists to Nazis, communists, the Taliban, and Satan. Luskin himself has labeled materialists an "ominous force" that will "consume" people. William Dembski proudly sponsored an animation that used fart noises to make fun of Judge Jones, who decided the Kitzmiller v. Dover case.

Our nomination for authoritarian high school principal of the month goes to Thomas Murray, principal of Danvers High School in Danvers, Massachusetts, who has chosen to ban the word "meep" from the campus.

Students reportedly had been using the nonsense word to disrupt classes. But isn't disrupting class already an offense at the school? Why would a word need to be banned, too?

Instead of using this opportunity to talk about free speech and preserving a good learning environment, the principal chose a heavy-handed and authoritarian approach to the problem. Shame on him.

The people they interviewed included neuroscientist Christof Koch, ethologist Colin Allen, primatologist Frans de Waal, and philosopher Colin McGinn. Now, who do you suppose had the most moronic things to say? Take a guess.

No surprise, it was the philosopher. Whenever scientific subjects are discussed, you can count on some philosopher to chime in with something really stupid. McGinn made all sorts of dubious unsupported claims, like "There are very strong reasons to think that reductionism is not true". He said, "I think there are problems of principle. In the very project you're trying to understand how the phenomenological might arise from the organic, because we're trying to bring together two different conceptual schemes, two different types of knowledge we have of the world, knowledge which we derive from first person awareness of our own consciousness and then the knowledge we have of the physical world, and these two types of knowledge simply don't fit together." Luckily Christof Koch was there to answer some of this kind of fuzzy thinking.

Unfortunately, the interviewer, Lynn Neary, didn't help things out. Although it should be obvious to anyone who thinks about it for even a few minutes that what we call "consciousness" is multifaceted, involving things like memory, planning, anticipation, modelling of the environment, and self-awareness, it took nearly half an hour before these ideas were brought out explicitly, and even after that, Neary persisted in conflating them. She seemed to want to have some very simple definition of what consciousness is before discussing it. Is it too much to ask that interviewers do a little homework before beginning their job?

If there's any consolation, at least they didn't interview Mario Beauregard.

Thursday, November 12, 2009

I attended the reunion for the Kitzmiller v. Dover trial over the weekend, which was held at Lauri Lebo's house in York Haven, PA. Lauri was a reporter for the York Daily Record at that time, and wrote the most intimate account of the trial in her book, The Devil in Dover. It is a terrific book, funny and sad at the same time, and definitely worth reading.

(As you may know, I played an extremely small role in this historic event - I had been asked to testify as a rebuttal witness against William Dembski. But Dembski withdrew from the trial, so my testimony was never needed.)

Lauri Lebo lives with the folk-rock-country musician Jefferson Pepper in two houses in rural Pennsylvania. I stayed in the famous beer can house, which houses the world's largest collection of beer cans. (I stayed in the German room, in case you want to know.)

I got to meet some of the important figures of the trial for the first time, including Vic Walczak of the ACLU, Richard Katskee of Americans United for the Separation of Church and State, and some of the plaintiffs, including Bryan Rehm, Cynthia Sneath, and Steven Stough. (There were others, but I'm bad with names.) And I got to see old friends, including the NCSE's Genie Scott, superstar biologist Ken Miller, and Behe-destroying lawyer Eric Rothschild.

Above: me with Genie Scott and some beer cans.

Above: Ken Miller.

In the evening there was a concert at the very cool Midtown Scholar Bookstore in Harrisburg, PA. (If you are ever in the area, this is definitely a place to visit. I picked up three books about snakes for my youngest son, who is a snake enthusiast, and two books about intelligent design for my anti-evolution & pseudoscience collection -- all at very reasonable prices.)

Above: ironic sign in the bookstore.

The concert featured a brief reading by Genie Scott, some terrific music by Jefferson Pepper and the Varmints of Heaven, a lecture by Kenneth Miller, and evolutionary rap by Baba Brinkman.

Above: Baba Brinkman and Eric Rothschild.

Above: rockin' out with Jefferson Pepper and the band. At right, on rhythm guitar, is York Daily Record columnist Mike Argento, who wrote some of the funniestnewspapercolumns about the Dover trial; he also has a blog.

Above: Baba Brinkman.

All-in-all, it was a fun weekend. Thanks to Lauri, Jeff, and the others who made it possible.

Friday, November 06, 2009

According to this article in the Press-Gazette, Mohamed El Naschie, former editor of the journal Chaos, Solitons, and Fractals is suing Nature because of a November 2008 article. That article, written by Quirin Schiermeier, raised the issue of the very large number of papers authored by El Naschie and published in that journal CSF, and the quality of those papers.

I don't think El Naschie has a case, but who knows in Britain, where libel laws are insane?

Monday, November 02, 2009

One of my long-term book projects is about mathematical theorems that give people fits. A good example is Cantor's theorem that the real numbers are uncountable. The proof is simple enough that you can explain it to a 10-year-old, but some adults simply don't get it, no matter how many times it is explained.

For example, see this thread over at Mark Chu-Carroll's blog. It just goes on and on, with one poster ("Vorlath") babbling away, but making no progress at all in comprehending this very simple proof.

I'd be interested in understanding the psychological mechanisms behind this kind of misunderstanding. It reminds me of the difficulty that some religious people appear to have in understanding evolution - you just go 'round and 'round with them, but they make no progress. Is it willful? That is, do they secretly know they are talking nonsense, but can't accept it because of their preconceptions? Or are they truly baffled?

Friday, October 23, 2009

12:14 PM I'm in a room in the Stata Center with about 50 others. We didn't get tickets to the event, held in MIT's Kresge Hall, but it is being broadcast here. People are talking about all the Secret Service agents around the campus, some people on roofs. Kids outside Kresge Hall, shouting "Obama!" over and over. Airspace near Logan was closed, with Air Force authorized to use deadly force against aircraft that didn't obey the temporary flight rules.

12:17 PM Stage is empty.

12:31 PM Presidential seal is affixed to podium.

12:42 PM Finally, some action. Susan Hockfield, President of MIT, is introducing Obama, talking about the MIT energy initiative.

12:46 PM Obama on the stage. Large amount of applause. "Thank you, MIT!" "It's always been a dream of mine to visit the most prestigous school in Cambridge, Massachusetts..." "Students put my motorcade on top of Building 10." "Everybody hands out periodic tables - what's up with that?"

12:50 PM He's talking about some of the energy innovations of MITEI: windows that funnel sunlight to solar cells, etc."You just get excited being and seeing these young people here at MIT" "It's the legacy of a nation who supported those intrepid few willing to take risks that might fail".

12:54 PM "There will be a debate of how to move from fossil fuels to renewable fuels ... but no question that we must do it.""Rising energy use imperils the planet." "Nations everywhere are racing to find new ways to produce and distribute energy.""I want America to be that nation" [to win the race]. Bill we passed in January "makes the largest investment in renewable energy in history".

12:56 PM Initiative by Deval Patrick will allow researchers to test very large wind turbine blades, the size of a football field, as part of the Recovery Act.

12:58 PM Recovery Act, the Stimulus Bill, is responsible for the largest increase in funding of science in history.

12:59 PM Renewable energy will be the profitable kind of energy in America. A bi-partisan issue. We'll have an energy system that is more efficient, cleaner, and independent. Safe nuclear power, sustainable biofuels, wind & solar power. Consensus is growing. Pentagon has declared energy-dependence a security threat.

1:02 PM Climate denier's only purpose is to "defeat or delay the change that is necessary". Pessimism is also a problem.We can do it. "This is the nation that pushed westward and looked skyward." "This is the nation that has led the world for 2 centuries in the pursuit of discovery."

Thursday, October 22, 2009

Roger Penrose is much smarter than I am. But I think he is completely wrong when he says

In my view the conscious brain does not act according to classical physics. It doesn’t even act according to conventional quantum mechanics. It acts according to a theory we don’t yet have. This is being a bit big-headed, but I think it’s a little bit like William Harvey’s discovery of the circulation of blood. He worked out that it had to circulate, but the veins and arteries just peter out, so how could the blood get through from one to the other? And he said, “Well, it must be tiny little tubes there, and we can’t see them, but they must be there.” Nobody believed it for some time. So I’m still hoping to find something like that—some structure that preserves coherence, because I believe it ought to be there.

We don't have any evidence at all that brains don't follow physical theories.

Tuesday, October 20, 2009

My sabbatical will end on July 1 2010, and I'm looking for good graduate students -at either the master's or the PhD level - in computer science who are interested in working on problems in automata theory, formal languages, combinatorics on words, complexity theory, number theory algorithms, or algebraic algorithms, beginning September 2010.

The University of Waterloo offers excellent financial support for graduate students. You can get information about our School of Computer Science and about the application process for admission to graduate school by clicking on the links.

If you're interested, send me e-mail (which you can find by going to my home page, and tell me what you've done and what you're interested in doing.

Sunday, October 18, 2009

One of my pet peeves is that if you see an error on a web page, and you want to notify someone in charge, it is usually difficult or impossible to do so. As a challenge, try to find the web page where you can report an error in Google Maps. It's not easy.

Here's another example. I recently bought a Canon scanner, and was curious about the technology. So I turned to their web pages, and found this page, which discusses it.

In the middle of the discussion, however, you find this bizarre sentence:

Yes, but I'll change it.

Obviously this was left in from the editing process. But how can you report it? Canon's web page doesn't have a "report error on this page" link, and their on-line form demands you pull down menus to pick a particular product (which isn't really apppropriate). Then, after I went through the whole process of filling out their form, and clicked "send", it reported that there was an error with their server.

I guess Canon is simply not interested in people pointing out silly errors on their pages.

I've never liked Bill Maher, and I've felt that way ever since I saw a video he did mocking Dan Quayle. Now to me, Dan Quayle exemplifies everything that is wrong about American politics: his frat-boy ignorance, his contempt for learning, his loony religious cult wife, etc., etc. So I was certainly prepared to like the video and laugh at Quayle. Instead, the treatment was so sneering, and so insulting, that I was left with a bad taste in my mouth and I was sorry I had wasted my time.

Sure, Maher is funny sometimes. But a lot of the time he is just ignorant. And now Orac has been showing us in detail that Maher is a raving lunatic when it comes to medical issues. How he was ever given the Richard Dawkins Award is beyond me.

Wednesday, October 14, 2009

I suppose we should be grateful that a Russian court has ruled against a descendant of Joseph Stalin in a suit brought by Stalin's grandson against Novaya Gazeta because the paper described Stalin as a "bloodthirsty cannibal".

What gets me is that apparently you can sue under Russian law for defamation against a dead person. That's a law that's ripe for abuse.

If this trend is adopted elsewhere, we can expect see a lawsuit brought by Alessandra Mussolini to restore the reputation of her grandfather, Benito; a lawsuit brought by Michael Reagan against Eric Alterman for calling his adopted father, Ronald Reagan, a "moron" and a "pathological liar"; and a lawsuit brought by the Catholic Church against Christopher Hitchens for his book about Mother Teresa, The Missionary Position.

William Lobdell is an American journalist. He rediscovered religion at age 29, became a "fully developed Christian", and got a job covering religion for the Los Angeles Times. As a reporter, he was exposed to the many misdeeds of organized religion, and in covering the religion beat, he eventually lost his religion - and wrote a book about it, called Losing My Religion (HarperCollins, 2009).

I wanted to like the book - but I didn't. Here's why.

1. The writing is clunky. Just because you're a journalist doesn't mean you can write a full-length book; the two crafts are very different. Reporters tend to write short, punchy sentences, and most don't have the time, inclination, or mandate to get deep into details. And reporters are always writing about other people, which means that when it comes time for self-reflection, they're often at a loss. The result is often self-indulgent (think of Anna Quindlen).

Here's an example:

So I began to pray. I asked God for a religion-writing job at the Los Angeles Times. I prayed for it in the morning, at night, and in between. On my weekly runs, I asked again. So did Hugh. We prayed and prayed and ran and ran -- and nothing happened. The prayers continued for four years. But my faith remained strong, and I didn't think about giving up.

And for a book by a reporter, there are surprising lapses. A Muslim football team is described on page 80 as being called the "Infitada". Where was the editor there?

2. Lobdell comes off as gullible and not particularly bright. I never got the impression that he thought deeply about his conversion -- or his deconversion. He calls C. S. Lewis "one of the great Christian minds of the 20th century", which doesn't convince me of Lobdell's acuity. And he actually liked The Screwtape Letters, one of the dreckiest books ever written. Lobdell writes that he was "moved" by the story of Charles Colson, former Watergate criminal who now spends part of his time lying about evolution and homosexuality.

He "eagerly read[s]" Lee Strobel's The Case for Christ, a book whose entire premise is so clearly dishonest that any reporter should immediately be tipped off. Lobdell writes that Strobel's book "chronicles the author's spiritual journey from skeptic to devout evangelical as he investigates the scientific and historical evidence for Christianity". But this is a very misleading description of what Strobel does. In his books, Strobel typically doesn't present evidence on both sides of the questions he considers -- we get just one side, the evangelical Christian side. This dishonest presentation doesn't escape skepticalreviewers, but it seems to have entirely escaped Lobdell.

Lobdell's conversion seemed more emotional than rational, more about how religion and the church made him feel. And his deconversion (see below) was largely along the same lines.

3. Lobdell seems impressed by the argument from authority. For example, he writes "I needed to hear Christians more intelligent than I who had the utmost confidence -- and evidence to back it up -- in what the Bible said, even those uncomfortable passages that most believers skip or ignore." But why didn't he make any effort to seek out people who didn't have that confidence, and also had evidence to back it up?

4. Lobdell doesn't seem to understand the role of a reporter. The job of a journalist is to "print the truth and raise hell", to "comfort the afflicted and afflict the comfortable". But not, it seems when reporting about religion. He writes, It's drilled into journalists that "if your mother tells you she loves you, better check it out." But such journalistic standards can't be applied to much of faith reporting. But it's precisely this mistaken belief that explains why so much religion reporting consists of little more than taking dictation from believers, instead of challenging them on their claims.

Here's an example: Lobdell writes, The worst a cynic could say about them [Billy Graham and Rick Warren] is that they encourage belief in things that might not be true. Really? That is the worst that a cynic could say about them?

5. His deconversion, when it comes, comes for the wrong reasons. He didn't give up Christianity because its claims are false or not supported by the evidence, but largely because of the wrongdoing of many Christians (especially Catholic priests). It wasn't an intellectual decision, but an emotional reaction to the wrongdoing by Michael Harris, Michael Pecharich, John Geoghan, and other priests. While we agree that the Catholic child abuse scandals are symptomatic of a unredeemably corrupt institution, I don't agree that these scandals are a particularly good reason for giving up Christianity. There are so many better reasons!

To be fair, there are also some things about the book that I liked. Lobdell appears to have done some genuinely good investigative work on Catholic child abuse scandals, and he wasn't scared off by the hostile reaction of many Catholics. He also broke the story on Paul Crouch's attempt to buy the silence of an employee about their sexual encounter. But in the end, I found the book unsatisfying. I hope that wherever his future career takes him, William Lobdell makes more of an effort to investigate claims skeptically, and to rely more on reason and less on emotion.